README.md

Methods

The author M.C. Ion shared a crayfish pathogen dataset suited for open access as an excel xlsx file GloBI_interactions.xlsx in globalbioticinteractions/globalbioticinteractions#1023 (comment) on 2024-11-14 (14-Nov-2024).

This resource was tracked using Preston, a biodiversity data tracker using:

preston track https://github.com/user-attachments/files/17749361/GloBI_interactions.xlsx

Following, the tracked xlsx file version was transformed into a tsv file using:

cat xlsx2tsv.sh | preston bash

The provenance logs of these tracking and processing events are stored in data/. A copy of the data transformation script xslx2tsv.sh is shown below, as extracted using:

preston cat hash://sha256/ba230547a13ddebdea3fea15868fe593d1fd95705c375c6a27bd5c7d2691aba8

producing:

#!/bin/bash
#
# transforms a version of the first xslx resource found into tsv stream 
#

preston ls\
 | grep hasVersion\
 | grep xlsx\
 | head -1\
 | preston xlsx-stream\
 | mlr --ijson --otsvlite cat

and resulted in ion2024-crayfish-pathogen.tsv with content id hash://sha256/5db7a5efba64aec29f9bd4356e9ff1765c61858bfc33e792e21e289508dcec38 as described in provenance log with content id hash://sha256/5e95f53f219f3470eecd3eafb5b74fcaa04c08142b27102fabe393399ebd887f.

Following, globi.json was created to help Global Biotic Interactions (GloBI, https://globalbioticinteractions.org) index the dataset derived from:

Ion MC, Bloomer CC, Bărăscu TI, Oficialdegui FJ, Shoobs NF, Williams BW, Scheers K, Clavero M, Grandjean F, Collas M, Baudry T, Loughman Z, Wright JJ, Ruokonen TJ, Chucholl C, Guareschi S, Koese B, Banyai ZM, Hodson J, Hurt M, Kaldre K, Lipták B, Fetzner JW, Cancellario T, Weiperth A, Birzaks J, Trichkova T, Todorov M, Balalaikins M, Griffin B, Petko ON, Acevedo-Alonso A, D’Elía G, Śliwińska K, Alekhnovich A, Choong H, South J, Whiterod N, Zorić K, Haase P, Soto I, Brady DJ, Haubrock PJ, Torres PJ, Şadrin D, Vlach P, Kaya C, Woo Jung S, Kim J, Vermeersch XHC, Bonk M, Guiaşu R, Harlioğlu MM, Devlin J, Kurtul I, Błońska D, Boets P, Masigol H, Cabe PR, Jussila J, Vrålstad T, Beresford DV, Reid SM, Patoka J, Strand DA, Tarkan AS, Steen F, Abeel T, Harwood M, Auer S, Kelly S, Giantsis IA, Maciaszek R, Alvanou MV, Aksu Ö, Hayes DM, Kawai T, Tricarico E, Chakandinakira A, Barnett ZC, Kudor ŞG, Beda AE, Vîlcea L, Mizeranschi AE, Neagul M, Licz A, Cotoarbă AD, Petrusek A, Kouba A, Taylor CA, Pârvulescu L. 2024. World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens. PeerJ 12:e18229 https://doi.org/10.7717/peerj.18229